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United States Department of Agriculture

Agricultural Research Service

Research Project: USING THE GENOME TO UNDERSTAND IMMUNOGENETICS OF POULTRY

Location: Avian Disease and Oncology Laboratory

Title: Poultry Genome Sequences: Progress and Outstanding Challenges

Authors
item Dodgson, Jerry -
item Delany, Mary -
item Cheng, Hans

Submitted to: Cytogenetics and Genome Research
Publication Type: Review Article
Publication Acceptance Date: January 7, 2011
Publication Date: February 19, 2011
Citation: Dodgson, J.B., Delany, M.E., Cheng, H.H. 2011. Poultry genome sequences: progress and outstanding challenges. Cytogenetics and Genome Research. p. 1-8. Available: http://content.karger.com/ProdukteDB/produkte.asp?Aktion=ShowAbstract&ArtikelNr=324413&Ausgabe=255102&ProduktNr=224037.

Interpretive Summary: Our biological understanding of poultry has been greatly enhanced by the generation of the chicken and turkey genome sequences. Not only do the genome sequences provide the complete “parts list” of each bird, a growing number of tools especially ultra high throughput “next generation sequencers” are dramatically enhancing the rate of gain of information and their application. In this review, we describe how the genome sequences were developed, the interesting findings, and the challenges that lie ahead in the near future.

Technical Abstract: The first build of the chicken genome sequence appeared in March 2004 – the first genome sequence of any animal agriculture species. That sequence was done primarily by whole genome shotgun Sanger sequencing, along with the use of an extensive BAC contig-based physical map to assemble the sequence contigs and scaffolds. Subsequent sequencing and mapping efforts have improved upon that first build, and efforts continue in search of missing and/or unassembled sequence, primarily on the smaller microchromosomes and the sex chromosomes. In the past year, a draft turkey genome sequence of similar quality has been obtained at a much lower cost primarily due to the development of “Next Generation Sequencing” or NGS techniques. However, assembly of the sequence contigs and scaffolds still depended on a detailed BAC contig map of the turkey genome that also utilized comparison to the existing chicken sequence. These two land fowl (Galliformes) genomes shows a remarkable level of similarity, despite an estimated 30-40 million years of separate evolution since their last common ancestor. Among the advantages offered by these sequences are routine re-sequencing of commercial and research lines to identify the genetic correlates of phenotypic change (for example, selective sweeps), a much improved understanding of poultry diversity and linkage disequilibrium, and access to high density SNP typing and association analysis, detailed transcriptomic and proteomic studies, and the use of genome-wide marker-assisted selection to enhance genetic gain in commercial stocks.

Last Modified: 4/20/2014